Kaempfer stayed two years in Japan, during which time he twice visited Edo and the Shogun Tokugawa Tsunayoshi there. When he visited Buddhist monks in Nagasaki in February 1691, he was the first western scientist to describe the tree Ginkgo biloba - scientists at the time thought that all Ginkgo species were extinct. He brought some Ginkgo seeds back that were planted in the botanical garden in Utrecht and can still be seen today. During his stay in Japan, his tact, diplomacy and medical skill overcame the cultural reserve of the Japanese, and enabled him to elicit much valuable information. In November 1692 he left Japan for Java.

As the English factory had been discontinued, the Dutch were now the only Europeans remaining in Japan. They did not escape suspicion, notwithstanding their attempts to make it plain that their religion was very different from that of the Spanish and Portuguese. In 1640, they came very near to getting into serious trouble through having inscribed the Christian date on a new warehouse they erected in Hirado. It may be, as suggested by Kaempfer, that this edifice, being unusually high and built of stone, was suspected of being made as much for a fortress as for a warehouse. Some of the enemies of the Dutch took this occasion for having an official inspection of the factory, turning over all the goods in hope that some religious wares might be found that would serve as an excuse for making an armed attack upon the merchants. Nothing of the kind was discovered, but orders were given that the warehouse bearing the obnoxious inscription should be torn down. The Dutch director has the good sense to comply and thus a conflict was avoided. The next year the factory was removed to Nagasaki. The Dutch has long desired to gain entrance to this port, but they soon found that, instead of the comparative freedom they had enjoyed in Hirado, they were to be hardly better than prisoners on the little island of Deshima, almost entirely cut off from communication with the Japanese, and hampered by many annoying regulations. Though these varied from time to time, they were in general for the next two centuries very much the same that are described by such writers as Thunberg, Kaempfer, and Siebold. When a Dutch ship arrived it had to give over its rudder and armament to the Japanese. A list of all persons on board was required, and frequent inspections were made to see that none were absent. Bibles, prayer books, and other objects having connection with the Christian religion were enclosed in a chest to be put in the care of the Japanese, or else hidden where it would escape their notice. All persons who went on shore were carefully searched to see that they carried no contraband goods. At one time the captains of ships were exempt from such inspection. It is said that they became noted for their corpulency; cloaks and trousers being made of such immense proportions that they afforded room for a good-sized cargo to be taken to and from shore in the three visits that were made each day. Thunberg says that sometimes the captains went so heavily loaded that they had to be supported under the arms by sailors who walked at their side.
Apparently persecution had attained its object and wholly extirpated the religion against which is was directed. So it seemed to Europeans, save as there remained among Roman Catholics a lingering hope, nourished by one or two incidents hereafter to be noted that some secret believers in Christianity yet remained; so it seemed to the Japanese, except as now and then suspicion arose against the inhabitants of certain villages whose customs had some strange peculiarities. References to the hated religion were not permitted in books, and its very name might have been almost forgotten were it not written so prominently on the public proclamation-boards of every town. As soon as a child could read, he saw upon the boards that the KIRISHITAN JASHU-MON (Evil Sect of Christianity) was strictly prohibited, and when he asked what this meant, he was told by his parents about the wily scheme of the barbarian nations that sought to gain possession of Japan by means of a religion that was a strange compound of foolish doctrines and powerful magic.

Kirishitan (吉利支丹, 切支丹, 鬼利死丹, キリシタン?), from Portuguese cristão, referred to Roman Catholic Christians in Japanese and is used as a historiographic term for Roman Catholics in Japan in the 16th and 17th centuries. Christian missionaries were known as bateren (from the Portuguese word padre, "father") or iruman (from the Portuguese irmão, "brother"). Both the transcriptions 切支丹 and 鬼利死丹 came into use during the Edo Period when Christianity was a forbidden religion. The Kanji used for the transcriptions have negative connotations.

Thus the close of this stage in the history of Christianity in Japan lift it as a religion that seemed to have been thoroughly defeated and whose very name was enough to excite the derision and hatred of those that heard it.

Silence (沈黙, Chinmoku) is a 1966 novel of historical fiction by Japanese author Shusaku Endo. It is the story of a Jesuit missionary sent to seventeenth century Japan, who endured persecution in the time of Kakure Kirishitan (“Hidden Christians”) that followed the defeat of the Shimabara Rebellion. The recipient of the 1966 Tanizaki Prize, it has been called “Endo’s supreme achievement” and “one of the twentieth century’s finest novels”. Written partly in the form of a letter by its central character, the theme of a silent God who accompanies a believer in adversity was greatly influenced by the Catholic Endo’s experience of religious discrimination in Japan, racism in France and debilitating tuberculosis.
Plot summary:

Young Portuguese Jesuit, Sebastião Rodrigues (based on the historical figure Giuseppe Chiara) is sent to Japan to succor the local Church and investigate reports that his mentor, Fr. Cristóvão Ferreira, has committed apostasy. (Ferreira is a historical figure, who apostatized after torture and later became a Zen Buddhist monk and wrote a treatise against Christianity.)
Fr. Rodrigues and his companion Fr. Francisco Garrpe arrive in Japan in 1638. There they find the local Christian population driven underground. Security officials force suspected Christians to trample on fumie, which are crudely carved images of Christ. Those who refuse are imprisoned and killed by anazuri (穴吊り), being hung upside down over a pit and slowly bled. Those Christians who do step on the image to stay hidden are deeply shamed by their act of apostasy. The novel relates the trials of the Christians and increasing hardship suffered by Rodrigues, as more is learnt about the circumstances of Ferreira’s apostasy. Finally, Rodrigues is betrayed by the Judas-like Kichijiro. In the climax, as Rodrigues looks upon a fumie, Christ breaks his silence:“Yet the face was different from that on which the priest had gazed so often in Portugal, in Rome, in Goa and in Macau. It was not Christ whose face was filled with majesty and glory; neither was it a face made beautiful by endurance to pain; nor was it a face with strength of a will that has repelled temptation. The face of the man who then lay at his feet [in the fumie] was sunken and utterly exhausted…The sorrow it had gazed up at him [Rodrigues] as the eyes spoke appealingly: “Trample! Trample! It is to be trampled on by you that I am here.”
Adaptations:
Masahiro Shinoda directed the 1971 film Chinmoku, an adaptation from the novel.
In May 2007, American film director Martin Scorsese announced his intention to shoot a film based on the book in summer 2008. On 2 February 2009 it was announced in Empireonline.com that Daniel Day-Lewis and Benicio del Toro have been signed to star in Scorsese’s film adaptation. The Internet Movie Database states the expected U.S. release date as 2011.